Hi all, Just a simple question on how GOHyperG calculates hypergeometric p-values - is the test one-tailed or two-tailed? and what would be the reason for using either of them? Cheers, Suraj Menon PhD Student Department of Pathology Henry Wellcome Building School of Medicine Cardiff University Heath Park Cardiff CF14 4XN Tel: +44 29 2074 3979 Email: MenonS1 at Cardiff.ac.uk

Hi Suraj, Suraj Menon wrote: > Hi all, > > Just a simple question on how GOHyperG calculates hypergeometric p-values - > is the test one-tailed or two-tailed? > and what would be the reason for using either of them? The test is one-tailed. See ?HyperGParams-class, in particular the testDirection slot. In general you would want to use a one-tailed test because you are testing a particular hypothesis (e.g., certain GO terms are over-represented) rather than a more general hypothesis (e.g., certain GO terms are represented at a level not consistent with their abundance in the universe from which they were selected). In addition, a one-tailed test will be more powerful. I suppose one might want to do a two-tailed test if there really were no hypothesis being tested, but instead the goal was to see "what's going on" in a certain experimental system. Best, Jim > Cheers, > > > Suraj Menon > PhD Student > Department of Pathology > Henry Wellcome Building > School of Medicine > Cardiff University > Heath Park > Cardiff CF14 4XN > > Tel: +44 29 2074 3979 > Email: MenonS1 at Cardiff.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald Affymetrix and cDNA Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Thanks, Jim - that was quite useful. Here is a little something for your amusement- http://papers.ssrn.com/sol3/papers.cfm?abstract_id=946199 Cheers -Suraj >>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> 18/07/07 2:30 PM >>> Hi Suraj, Suraj Menon wrote: > Hi all, > > Just a simple question on how GOHyperG calculates hypergeometric p-values - > is the test one-tailed or two-tailed? > and what would be the reason for using either of them? The test is one-tailed. See ?HyperGParams-class, in particular the testDirection slot. In general you would want to use a one-tailed test because you are testing a particular hypothesis (e.g., certain GO terms are over-represented) rather than a more general hypothesis (e.g., certain GO terms are represented at a level not consistent with their abundance in the universe from which they were selected). In addition, a one-tailed test will be more powerful. I suppose one might want to do a two-tailed test if there really were no hypothesis being tested, but instead the goal was to see "what's going on" in a certain experimental system. Best, Jim > Cheers, > > > Suraj Menon > PhD Student > Department of Pathology > Henry Wellcome Building > School of Medicine > Cardiff University > Heath Park > Cardiff CF14 4XN > > Tel: +44 29 2074 3979 > Email: MenonS1 at Cardiff.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald Affymetrix and cDNA Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.